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15
votes
22
replies
1.8k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
26 days ago • updated 5 days ago
Chris
• 0
0
votes
18
replies
2.4k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.1 years ago by
lea
• 0
6
votes
16
replies
2.2k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 1 day ago by
Michael Love
41k • written 4.6 years ago by
hsbio
▴ 10
1
vote
13
replies
244
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
3 days ago • updated 17 hours ago
fernanda.backsouza
▴ 10
12
votes
12
replies
761
views
Why p value inconsistent when using different number of pathway score?
limma
updated 3 days ago by
Robert Castelo
★ 3.3k • written 4 days ago by
Chris
• 0
6
votes
12
replies
4.7k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 3 days ago
shepherl
3.8k
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 6 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
6
votes
10
replies
1.5k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 6 days ago by
i.atanasoai
• 0 • written 14 months ago by
mohammedtoufiq91
▴ 10
4
votes
8
replies
341
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 6 days ago by
Peter Hickey
▴ 740 • written 14 days ago by
Juan Higareda
• 0
0
votes
8
replies
217
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 8 hours ago by
swbarnes2
★ 1.3k • written 1 day ago by
Aaliya
• 0
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 2 days ago by
hortense96
• 0 • written 7.7 years ago by
dmcleanuk
▴ 30
0
votes
7
replies
386
views
DESeq filtering specific to contrasts
DESeq2
updated 5 days ago by
Michael Love
41k • written 9 weeks ago by
Emma
• 0
0
votes
7
replies
611
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
7 weeks ago • updated 1 day ago
shepherl
3.8k
0
votes
7
replies
244
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
8 days ago • updated 2 days ago
hortense96
• 0
4
votes
6
replies
327
views
FilterByExpr low counts with small sample size
edgeR
7 days ago • updated 2 days ago
Jonathan
▴ 10
0
votes
5
replies
208
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 23 hours ago by
James W. MacDonald
65k • written 3 days ago by
Gayatri
• 0
2
votes
5
replies
695
views
DESeq2 setting significant p-value
DESeq2
updated 5 days ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
2
votes
5
replies
139
views
get BM error
ensembldb
updated 22 hours ago by
James W. MacDonald
65k • written 1 day ago by
Fara
• 0
6
votes
5
replies
398
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC
minifi
written 7 weeks ago by
Kim
• 0
11
votes
5
replies
7.3k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 6 days ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
0
votes
4
replies
194
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
7 days ago • updated 5 days ago
lonn
• 0
0
votes
4
replies
131
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
6 days ago
sropri
• 0
0
votes
4
replies
229
views
DEG with low counts
DESeq2
updated 6 days ago by
Michael Love
41k • written 10 days ago by
Rajat
• 0
1
vote
4
replies
129
views
minfi::read.metharray.exp
minfiData
minfi
updated 1 day ago by
Basti
▴ 780 • written 2 days ago by
clacarion
• 0
1
vote
4
replies
143
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 2 days ago by
James W. MacDonald
65k • written 6 days ago by
Mirella Aurora
• 0
0
votes
3
replies
1.1k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 3 days ago by
lauryfriese932
• 0 • written 18 months ago by
Maria Doyle
▴ 70
0
votes
3
replies
222
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 6 days ago by
W. Evan Johnson
▴ 850 • written 13 days ago by
schlumbohm
• 0
0
votes
3
replies
128
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 6 days ago by
Gordon Smyth
50k • written 6 days ago by
prity6459
• 0
0
votes
3
replies
102
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 5 days ago by
James W. MacDonald
65k • written 6 days ago by
bas_work
▴ 30
3
votes
3
replies
284
views
permutation test in edgeR
rna-seq
edgeR
updated 4 days ago by
Gordon Smyth
50k • written 17 days ago by
Netanel
• 0
3
votes
3
replies
156
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 2 days ago by
Michael Love
41k • written 2 days ago by
WardDeb
• 0
1
vote
3
replies
811
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 1 day ago by
Guangchuang Yu
★ 1.2k • written 13 months ago by
ruiqi.li
▴ 10
1
vote
3
replies
84
views
Different Shrunk Log2FC according with reference
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
andrebolerbarros
▴ 20
2
votes
3
replies
101
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 1 day ago by
James W. MacDonald
65k • written 1 day ago by
bandconductor
• 0
0
votes
3
replies
99
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
updated 47 minutes ago by
James W. MacDonald
65k • written 1 day ago by
winwater0928
• 0
0
votes
2
replies
105
views
featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumpe…
metaMSdata
2 days ago • updated 7 hours ago
shuwangxinze1996
• 0
0
votes
2
replies
152
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
5 days ago • updated 3 days ago
catv
• 0
0
votes
2
replies
766
views
Job:
Bioinformatics Laboratory Head in AI or machine learning (WEHI, Australia)
bioconductor
artificialintelligence
JobPosting
machinelearning
written 8 months ago by
Gordon Smyth
50k
3
votes
2
replies
154
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 3 days ago by
Guido Hooiveld
★ 3.9k • written 5 days ago by
fernanda.backsouza
▴ 10
0
votes
2
replies
91
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
6 days ago
prity6459
• 0
0
votes
2
replies
31
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 34 minutes ago by
James W. MacDonald
65k • written 1 hour ago by
Alexandre
• 0
0
votes
2
replies
236
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
24 days ago • updated 5 days ago
isaac.vock
• 0
2
votes
2
replies
139
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 6 days ago by
James W. MacDonald
65k • written 6 days ago by
sansan
• 0
1
vote
2
replies
75
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
1 day ago • updated 6 hours ago
ATpoint
★ 4.0k
0
votes
2
replies
898
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.2 years ago by
araaaju
• 0
1
vote
2
replies
124
views
Error in champ.load(): The following specified files do not exist
ChAMP
7 days ago • updated 6 days ago
Sherin
• 0
1
vote
2
replies
925
views
DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE, : NA/NaN/Inf in foreign function call (arg 1)"
DMRcate
Gviz
updated 2 days ago by
Tim Peters
▴ 170 • written 14 months ago by
jose.ramirez1
▴ 10
1
vote
2
replies
180
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
7 days ago • updated 6 days ago
Le
• 0
1
vote
2
replies
219
views
How to retrieve detailed regression results from deseq2
DESeq2
14 days ago • updated 5 days ago
Weiqian
▴ 10
1
vote
1
reply
70
views
Citation for edgeR user guide
edgeR
updated 1 day ago by
Gordon Smyth
50k • written 1 day ago by
k___
▴ 30
74 results • Page
1 of 2
Recent ...
Replies
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
James W. MacDonald
65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
Comment: Reproducibility issue with scran together with lapply and BiocParallel
by
ATpoint
★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Votes
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
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